Probes and Primers

DNA Probes and Primer Sets

DNA Clones

We maintain stocks for over 2000 probes developed in our lab of which 1500 have mapping data in one or more species. These probes are predominantly cDNA probes derived from oat and barley. All of our probes are distributed by the USDA National Probe Repository in Albany, CA. They may be obtained by sending email to probes@pw.usda.gov

ANCHOR PROBES

For our comparative mapping research we systematically evaluated a large portion of our probes on seven species (rice, wheat, barley, oat, maize, sorghum, and sugarcane). A subset of those that gave good hybridization signal on a majority of species was designated as "anchor probes" for comparative mapping and are listed below. These probes hybridize to loci that are well distributed across most of the genome maps. These probes are distributed as a set by Dr. Susan McCouch. Send requests by email to: srm4@cornell.edu

BCD98, BCD134, BCD135, BCD147, BCD207, BCD348, BCD349, BCD386, BCD450, BCD454, BCD738, BCD808, BCD828, BCD855, BCD880, BCD926, BCD1072, BCD1087, BCD1261, BCD1421, BCD1823, CDO17, CDO20, CDO36, CDO38, CDO59, CDO78, CDO87, CDO89, CDO98, CDO105, CDO118, CDO122, CDO127, CDO202, CDO204, CDO241, CDO244, CDO328, CDO344, CDO345, CDO365, CDO385, CDO393, CDO395, CDO400, CDO405, CDO407, CDO412, CDO455, CDO456, CDO457, CDO459, CDO460, CDO470, CDO475, CDO497, CDO507, CDO516, CDO520, CDO524, CDO534, CDO542, CDO545, CDO580, CDO590, CDO595, CDO686, CDO718, CDO783, CDO795, CDO920, CDO938, CDO941, CDO962, CDO1081, CDO1160, CDO1173, CDO1328, CDO1338, CDO1380, CDO1387, CDO1395, CDO1417, CDO1508, RZ2, RZ14, RZ53, RZ69, RZ87, RZ141, RZ143, RZ144, RZ166, RZ206, RZ242, RZ244, RZ251, RZ261, RZ273, RZ296, RZ323, RZ329, RZ382, RZ387, RZ390, RZ395, RZ397, RZ400, RZ403, RZ404, RZ413, RZ421, RZ444, RZ446, RZ455, RZ474, RZ476, RZ500, RZ508, RZ509, RZ516, RZ525, RZ537, RZ538, RZ543, RZ567, RZ574, RZ583, RZ588, RZ590, RZ596, RZ599, RZ612, RZ614, RZ630, RZ670, RZ672, RZ682, RZ698, RZ740, RZ753, RZ783, RZ797, RZ816, RZ836, RZ892, RZ900, RZ912, RZ952, RZ953, RZ995, WG110

MICROSATELLITE MARKERS

References:

Ma, Z.Q. , M.S. Röder, and M.E. Sorrells. 1996. Frequencies and sequence characteristics of di-, tri, and tetra-nucleotide microsatellites in wheat. Genome 39:123-130.

Röder, M. S., J. Plaschke, S. U. König, A. Böner, M. E. Sorrells, S. D. Tanksley, and, M.W. Ganal. 1995. Abundance, variability, and chromosomal location of microsatellites in wheat. Mol. Gen. Genet. 246:327-333.

Table 1. Microsatellites that produced polymorphisms, their primers, the expected product size and GenBank accession numbers.

Micro-satellite Primers Repeat sequences Expectedsize* (bp) Accession numbers

TCT4 GTTAGTGCTAGGTTTAGGTG (AGG)3(AGA)14 293 U36888

GAGAACTGTTGCTGCTG

AC1 CACAAATCGGCGAAAAC (TG)18 157 U36889

GCTGTAAACTCCATTGTTTGG

AC14 GAAAGACCAAGTGAAACACG (TG)7T3(GT)18 376 U36890

TGAATAAAGAAGGGAGCATC

AC22 AGAACAGTCTTCTAGGTTAG (TC)15(AC)12 139 U36891

CGAGGGACAGACGAATC

AC29 CCTAGTTAGCGAGAGCAATG (TG)8TT(TG)6, (GA)5, 350 U36892

GGTGGTTTGAAAAAGAGATG (AG)14, (TG)10(AG)17

AG10 GGTGATGAGTGGCACAGG (CT)13 129 U36893

CCCAACAGTTGCAGAAAATTAG

AG24 GGACGAATGAAAAATTCCCAGG (TC)17C2(TC)6(C)2(TC)9 204 U36894

GAGCGGTCTTCGGACTTTC

* Expected product size for Geneva wheat.

Table 2. Conditions for PCR amplification, allele number and the chromosome locations of the polymorphic fragments.

Micro- PCR conditions Allele Chromosome satellite Annealing T° MgCl2 (mM) number location

TCT4 54 2.0 3, 4 ND

AC1 52 2.5 5 7BS

AC14 56 3.0 2 3DL

AC22 50 3.0 6 6BS

AC29 56 2.5 4 2AS or 4BSa

AG10 52 1.5 3 1AS

AG24 50 2.5 5 2BL

Chromosome location of AC29 could not be determined due to the lack of nullisomics of 2A and 4B, and ditelosomics 2AS and 4BS.

Other Microsatellite Primers that did not Produce Expected Products:

AC4 AGCAGATGGCAAAGATC

AC4 CGGTAGGTTCGCTTCGG

AC7 ATTGAGGGAGGGTGTTAGTC

AC7 TATATAGGATCCGTCTCGTC

AC11 CAGTGGCAGCTCCATCC

AC11 CGAGAATAAGGGGATTGACAAC

AC12 CCAGTCGGACACCCCTG

AC12 GCTTCATGGAGCTGGTG

AC15 AGAACGACGGGGACAAG

AC15 GCACTATTTTTTGGGCTTG

AC24 GAACACCATCACCAACTCTG

AC24 GGTGCCACCCTACTCCTTC

AC25 CCCACACACACTTAGACTCC

AC25 GGAATTTGTCCATGTTATGC

AC30 GACACACAGTGAGACTGGAGAAG

AC30 GCAATCTCGTCGGTTTTCAC

AC33 CGTGTGCGATGCACCAC

AC33 CGTTGACGGGGACCTTC

ACB AGATTAGCATCCAACACC

ACB TCCCCGTGAGTAAGTTG

AG20 CATGGGTTCGTGTGCCAG

AG20 TCATCAAGATCAATCAAGCAGG

AG22 CCTGATGGGGGTTGTGG

AG22 TGAATGGGGGCACTAGATG

AG25 CATACATAGTGTGCGAGAGATACC

AG25 GCAGAGCGGCACGAGTG

AG31 CACAAACCAACAATCCACCTAG

AG31 GTCGCACATAAGTGCCCTG

AG49 AGATAGAGAGGGGAAAATACC

AG49 CCACGATGAGGAGGGAG

AG50 CTGCTGCCTGACTTTAGGTTC

AG50 TTCTCCCTCTCCCTCCATC

OLIGO-PRIMER SEQUENCES

We have end-sequenced a number of our cDNA clones and designed primers that amplify a wheat fragment. These primer sequences are listed below:

BCD129 CAACAATATGGGCATTACAT

BCD129 CGAGGAGTTCTACAAATCAT

BCD175.1 CATGGAGGATGTCGCTCATC

BCD175.1 TGTAAACCAGCCATCCGACA

BCD175.11 CGAACAAATACAGCCAGAGA

BCD175.11 CGCTCATCTATGTGAAATAC

BCD269 ATTCGGCACGAGCAATGGCT

BCD269 CCAACACACACCATTACACC

BCD304 ACA TCA CGG CAC ACT GAA AT

BCD304 GAT TAG CAG GTT GAC AGA GC

BCD327 L:GGCACGAGGCACAAACTTGA

BCD327 R:ACGAGCAGAAGCCAAGCCAA

BCD327.11 ACGAGCAGAAGCCAAGCCAA

BCD327.11 GGCACGAGGCACAAACTTGA

BCD402.1 ACCTTGATCACCTGATCCAC

BCD402.1 TGCCACAACGACGTGACGCA

BCD402.11 CAG TGG CAG CGA GCG ATT TA

BCD402.11 CCT GGT GGG CAT CAA CTA CC

BCD402.12 CACCTGATCCACCTTCATGG

BCD402.12 TGACCGCATGCACCGTTGCC

BCD828 AACAGCTATGACCATG

BCD828 GTAAAACGACGGCCACT

CDO36 AGCCCTCGCCTAGCTCAG

CDO36 TCAAGCGAACCATCAGCGT

CDO63 CCACTGGCAGGATTTGCAAA

CDO63 GGCACGAGCGGATTTGTATC

CDO213 GGC AGT TGA ATG AGT TTG AG

CDO213 TAA TCA CGA GGT CAC TAA TC

CDO370 CCC TTG CCC TTC TTC TTC TG

CDO370 GCT CTC CGC CTG GAT ACA GC

CDO395 AAC TCG GTC GTT ACA AGA GC

CDO395 ACC CCA TCG GTC TGT CTA TG

CDO464 ATT GAG TTA GAA GGA GAG TG

CDO464 CAA AAG AGT TCA GGA AAG AT

CDO474 ACGTCCTCTCCAAGGCCAAT

CDO474 TTTGGACCGTTCAGAGTTGC

CDO475 CCT TCA CCT CGC TCC CTA CC

CDO475 GAC ACA TTG ACC GCA TCT TA

CDO479 GCG GAG TAG TAT TAG TCA CA

CDO479 TCT CAG GAG CAG GTC AGT TA

CDO506 ATA GTG GAG CAA AGA CTG TC

CDO506 TCA TTC AGA GGA AGA ACT GC

CDO541 ACA GAA ATG ACT CAC ACA GG

CDO541 AGA AAC ATA ACC GCA ACA TC

CDO545.1 CTAACCAGGAAACAACGACT

CDO545.1 CTTTGTTGTCAGAGTACAGC

CDO545.2 GGA ACT TCT TTG GAC ACC TG

CDO545.2 TTA GGA GAC TGC TGG ATT AT

CDO588.1 CGT GGC TTG CGT GCC TCT CC

CDO588.1 TCTCCAGACACATGCTCATT

CDO588.2 AAA AGA AAC GAC GAT GAC AC

CDO588.2 CGAGGCTGCTCCAATGGCTG

CDO662 AGCTCCAGAAGGCAAAGAAG

CDO662 CTTTTTACAGCAGGAGGCC

CDO662 L:CTTTTTACAGCAGGAGGCC

CDO662 R:AGCTCCAGAAGGCAAAGAAG

CDO673 ACG AGC GTC AGT CGG TCA CT

CDO673 GCC ATT GGT ATT GCG AGA GG

CDO749 GCGGAGTAGTATTAGTCACA

CDO749 TCTCAGGAGCAGGTCAGTTA

CDO770 AAG TAG TTG GAA GAA AGT TA

CDO770 AAT TTA CAG CAA TCA TTT CA

CDO1338 GCACTAAGGCATACACCAGT

CDO1338 GCTTTCCTTTTGCAGCAACA

CDO1338 L:GCTTTCCTTTTGCAGCAACA

CDO1338 R:ACAACTCCCCTTCACTGTTC

WG110.1 ACGGCGATCCGTCCACGAGC

WG110.1 TCTGATACACACCTCCAGCG

WG110.2 ATACAACAGGAGCCACTACA

WG110.2 CGAGGACATCGCTGAGAAGA

WG110.3 AGATTTAGGTGACACTATAGGACCGGGCTTGGGTTCC

WG110.3 GATAATACGACTCACTATAGGGAATTTTCTACTTCTC

WG114 ATC ACA ACA TTT CAG AGT TT

WG114 GGC TCA ATA GAA TAG TAT CA

WG178 ACCTCGATACGACGTTTGTC

WG178 TCACAAGCGGAGGTGCCAGG

WG181 AGATACAACCCAGCGTCAGT

WG181 CGGTCACTCTACTCAGTTTT

WG232.1 CCGCTTTCCTCAGTGTTTCA

WG232.1 TTCAACCCCAGGTATGCTGT

WG232.11 CCTCAGTGTTTCAGGGTAAA

WG232.11 TGGACTCGTGTTCAATAATG

WG241.1 CCAAGAAACAAGTTCCTGAC

WG241.1 CTGTGAGATGTAGGTGTAGC

WG241.11 GGA CTT GGT CAT CTG TGA GT

WG241.11 GTC TGG TAA TAA GCG GTA AT

WG464 AGGACTGTGAAGATGCTACT

WG464 AGTCCAAATGATGTCACAGG

WG530 CAA TGC TCC AAA TCT CAC CA

WG530 GAG ACC AAA GAT TCA ACA GC

WG541 AATTCGATCGCACCGTCGGA

WG541 TCCAACCAAAGGAACGAAGG

WG564.1 ACGAGGAGCACATACTACAT

WG564.1 CACTGGGAGCGGAGATACTA

WG564.2 ACTATGAAGAGATGGAAAAT

WG564.2 ACTGATCTTGGGGTTGTGTT

WG622 AGGTGGGACTGGAACCTGCATC

WG622 CTCCTGTCAAACTGTTCCCTGA

WG669 AAAGGAGGAGCCCAGTGATT

WG669 GAAGGAAAGGTTCCCCATCC

WG686.1 GCTGTTCATATAAAAGGAGA

WG686.1 TCGCTTTACCACAATTTCAG

WG686.11 CCA GCC ACC TTT TAC AGA GC

WG686.11 TCA GCG ACA CCC ACA TTT TC

WG719 AAG GTG AGG TAG ACG ACA GC

WG719 GAA AAC AAC AAA AAC AAA TC

WG940 GCACACACAAACGACGACGG

WG940 GCATTGCAATACAGTGAGTC

WG983.1 GTGTTATACTTGAGACTGGA

WG983.1 TTTGCTGGTATGCTTCAACG

WG983.11 AAA GAG AGA TAA GGA TGA TG

WG983.11 TGC AGT TGA CGA GAT ACT AT

WG996 AGC CCA GGT TCT ACA ACA AC

WG996 CCT TCA CTG ACC CCT AAA TA

WG1026.1 ATGGGATCACCTGGAGGATG

WG1026.1 TGCTAAACAAAGACTTGCTG

WG1026.11 CAG ATA CAT CAG TTC CAC TA

WG1026.11 CTT ATT CTT TTG CTA TGA GT